Comments on Sanford and Carter respond to PS participants

[PDPrice (Paul Price)]

@T_aquaticus

Hand-waves aren’t rebuttals.

I certainly agree.

[Timothy_Horton]

Yet all you ever post are hand waves to the scientific evidence. That’s the scientific evidence you don’t completely ignore becasue you can’t even think of a plausible hand wave.

[jeffb (Jeff)]

@PDPrice

I long ago availed myself of the “mute” feature to deal with his continual trolling. You won’t escape it either unless you do the same.

A Mute feature! Brilliant… and now implemented. Thank you!

[T_aquaticus]

@PDPrice

I certainly agree.

Then “it’s just too improbable” without any math or science behind is not sufficient. For example, compare junk DNA between humans and mice, which make up ~90% of each genome. There’s lots of mutations that separate them, and the chances of a new human mutation reverting the human sequence back to the ancestral sequence is very high.

[added in edit]

Coding regions showed strong sequence similarity [between the human and mouse genomes], with approximately 85% identity as previously reported (Makalowski et al. 1996; Makalowski and Boguski 1998, 1998a; Lamerdin et al. 1995; Koop and Hood 1994). In contrast, introns showed only weak sequence similarity with approximately 35% sequence identity, which is not much higher than the background rate of sequence identity in gapped alignments of random sequences.
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction - PMC

[Timothy_Horton]

@jeffb

A Mute feature! Brilliant… and now implemented. Thank you!

It’s the coward’s way of admitting they can’t explain the scientific evidence presented. One of the common tactics of ID-Creationists.

[PDPrice (Paul Price)]

@T_aquaticus

If you compare genomes between distantly related species you will find a lot of differences in junk DNA.

Those comparisons only succeed in assuming what you’re trying to prove, on multiple counts. For one thing they assume DNA is ‘junk’ (which it likely is not). And secondly they assume these species are in fact distantly related–the very thing under debate.

[T_aquaticus]

@PDPrice

Those comparisons only succeed in assuming what you’re trying to prove, on multiple counts.

Umm, no. 35% identity between human and mouse introns is observed, not assumed. That’s 65% different. This means there is a very high probability of new human mutations reverting those bases back to their ancestral sequence.

@PDPrice

And secondly they assume these species are in fact distantly related–the very thing under debate.

That’s a conclusion based on mountains of evidence. It’s not an assumption.

[John_Harshman]

@T_aquaticus

35% identity between human and mouse introns is observed, not assumed.

How would you even align such sequences to come up with a distance measure?

[T_aquaticus]

@John_Harshman

How would you even align such sequences to come up with a distance measure?

There’s an algorithm for that.

When two corresponding regions in the human and mouse are not very similar, GLASS does not necessarily produce the exact map between the regions. For that reason, the corresponding introns, coding, and non-coding exon fragments in human and mouse sequences were further realigned using the standard dynamic programming (SDP) alignment algorithm in order to compute more accurate local alignments for the purpose of compiling nucleotide similarity statistics.
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction - PMC

It may be a case of GIGO, but there it is nonetheless.

[Rumraket (Mikkel R.)]

@jeffb

Here’s the point: If GE is true, then your 700,000 horse genome is a problem for you .

Alternatively, you have a conflict between theory and observation.

On the one hand you have the assumption of a fixed and unchanging mathematical abstraction (a fixed and unchanging DFE of mutations) that implies all genomes should be continuously undergoing fitness decline.

And then you have the observation that there lived healthy horses 700,000 years ago, and modern horses still exist today that are healthy.

It seems to me this observation should cause you to doubt that your mathematical abstraction is correctly describing the reality you inhabit.

[Rumraket (Mikkel R.)]

@PDPrice

For one thing they assume DNA is ‘junk’ (which it likely is not).

The conclusion of junk is derived from evidence collected over decades, not assumed. You’ve had this explained to you many times before.

[Timothy_Horton]

@jeffb

GE causes you to question those 700,000 years.

Here’s the paper which describes how the horse remains in question were dated. They were found in strata dating 0.74 +/- 0.06 MYA as determined by three independent methods: fission track dating, paleomagnetic dating, and index fossils.

Gold Run tephra: a Middle Pleistocene stratigraphic and paleoenvironmental marker across west-central Yukon Territory, Canada

Feel free to post your evidence the three independent dating methods are all wrong.

[Faizal_Ali]

@jeffb

Here’s the point: If GE is true, then your 700,000 horse genome is a problem for you . As you’ve said yourself: " Why haven’t horses gone extinct from GE in 700,000 years? ". GE causes you to question those 700,000 years.

Of course, if we accept the fact that biology also applies to organisms other than horses, then we have to ask why, say, E.coli has not gone extinct after two weeks or so.

I’d still like an answer from a YEC scholar on this question, but it’s been quite difficult to get one.

[Giltil (Gilbert Thill)]

@glipsnort

Um, yeah. That’s talking about detectable, functional, selectable differences in genes. There is no question that humans are highly adapted, and that most individuals have largely optimal (or at least locally optimal) versions of those genes.

GE isn’t about that. It’s about undetectable, non-selectable differences in DNA. What GE doesn’t explain is why those mutations of that kind should consistently be deleterious.

Take the average human being today. Take the average human being let’s say 500 years later. Which one do you think will harbor the more deleterious mutations? Wouldn’t it be the later? And in that case, wouldn’t have he suffer from GE?

[Michael_Okoko]

@swamidass thank you for PS. I don’t fancy the idea of debating pseudoscientific ideas in public because it grants them illegitimate authenticity. However, you allow this on PS, giving the purveyors of fringe ideas a chance to defend themselves.

The most beautiful thing about it all is that these pseudoscientists flop when they defend their ideas, demonstrating why a large majority of scientists don’t think it’s wise to debate them at all.

As these rebuttals to the rebuttals of Sanford and Carter continue, it’s become obvious that GE proponents don’t have a strong basis for their claims.

Thank you @swamidass, @John_Harshman, @Rumraket, @chris_doesdna2018, @glipsnort and others.

@John_Harshman, @chris_doesdna2018, @glipsnort and @dsterncardinale, to resolve your differences on the issues being discussed, I suggest one of you start a new thread, where each person would define or explain the terms he thinks the others misunderstand, providing evidence to support the others really misunderstand that definition. I am learning from you guys, but the waters are a bit muddied now, so its best you all take a step back to review your thoughts.

[Timothy_Horton]

@Giltil

Take the average human being today. Take the average human being let’s say 500 years later. Which one do you think will harbor the more deleterious mutations? Wouldn’t it be the later? And in that case, wouldn’t have he suffer from GE?

No. As has been explained ad nauseum “deleterious” and “beneficial” can only be determined with reference to their effect on reproductive fitness in the local environment. With humans now our technology has become a huge part of our environment. Mutations which would have almost always killed us 2000 years ago are now routinely handled by modern medicine.

Do you have any evidence other large species like elephants, horses, cattle, etc. have more deleterious mutations now than they did 2000 years ago, or that those species are now less fit due to GE?

[Rumraket (Mikkel R.)]

@Giltil

Take the average human being today. Take the average human being let’s say 500 years later. Which one do you think will harbor the more deleterious mutations? Wouldn’t it be the later? And in that case, wouldn’t have he suffer from GE?

That’s a strange question because GE is not the only idea that says deleterious mutations can accumulate, so merely observing or expecting an accumulation of deleterious mutations under some circumstance can’t be taken, in and of itself, to imply that we are observing GE.

You must find some way to distinguish between whether you are observing actual GE (persistent, inevitable, and fixed fitness decline), or merely transient fitness decline due to other factors such as relatively rapid changes in the type or magnitude of selective pressure.

[John_Harshman]

@T_aquaticus

It may be a case of GIGO, but there it is nonetheless.

I would agree with the GIGO assessment. It might be good enough to get a very rough measure of similarity, but it’s dangerously close to fully randomized, considering that 25% similarity is randomized even using a Cavalli-Sforza (brain fart: Jukes-Cantor) model.

[T_aquaticus]

@John_Harshman

I would agree with the GIGO assessment. It might be good enough to get a very rough measure of similarity, but it’s dangerously close to fully randomized, considering that 25% similarity is randomized even using a Cavalli-Sforza model.

Completely agree. p hacking is a real thing, and statistically significant is not a synonym for meaningful.

Nonetheless, the point is that nature has already tested Sanford’s GE for us. Effectively neutral mutations have been accumulating in the mouse and human genome for millions of years to the point that a comparison of orthologous introns is nearly indistinguishable from a comparison of random sequence. Humans and mice are doing just fine.

This is in stark contrast to human and mouse exons where there is an average of 85% identity. A large difference in sequence conservation between exons and introns is exactly what we would expect from evolution and distantly related species, and I have yet to hear a compelling YEC’s explanation for why we see this pattern.

[glipsnort (Steve Schaffner)]

@Giltil

Take the average human being today. Take the average human being let’s say 500 years later. Which one do you think will harbor the more deleterious mutations?

As has already been pointed out, the overwhelmingly largest effect on the number of deleterious mutations will be the change in selection pressures. Aside from that, I would expect a very slight decrease in the number of deleterious alleles per person, thanks to the greater effectiveness of humanity’s currently large population size in removing deleterious alleles by purifying selection (assuming we manage to maintain a large population, which I don’t take as certain).

@Giltil

Wouldn’t it be the later?

Why? Why would NS not be removing deleterious mutations?